Division of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan.
Methods Mol Biol. 2023;2691:165-183. doi: 10.1007/978-1-0716-3331-1_13.
DNA methylation of promoter CpG islands silences their downstream genes, and enhancer methylation can be associated with decreased or increased gene expression. DNA methylation alterations in normal and diseased cells provide rich information, such as tissue origin, disease risk, patient response, and prognosis. DNA methylation status is detected by bisulfite conversion, which converts unmethylated cytosines into uracils but methylated cytosines very inefficiently. A genome-wide DNA methylation analysis is conducted by a BeadChip microarray or next-generation sequencing (NGS) of bisulfite-treated DNA. A region-specific DNA methylation analysis can be conducted by various methods, such as methylation-specific PCR (MSP), quantitative MSP, and bisulfite sequencing. This chapter provides protocols for bisulfite-mediated conversion, a BeadChip array-based method (Infinium), quantitative MSP, and bisulfite sequencing.
启动子 CpG 岛的 DNA 甲基化使其下游基因沉默，而增强子的甲基化可能与基因表达的减少或增加有关。正常和患病细胞中的 DNA 甲基化改变提供了丰富的信息，例如组织来源、疾病风险、患者反应和预后。DNA 甲基化状态通过亚硫酸氢盐转化来检测，该转化将未甲基化的胞嘧啶转化为尿嘧啶，但甲基化的胞嘧啶转化效率非常低。全基因组 DNA 甲基化分析通过 BeadChip 微阵列或亚硫酸氢盐处理的 DNA 的下一代测序 (NGS) 进行。通过各种方法（如甲基化特异性 PCR (MSP)、定量 MSP 和亚硫酸氢盐测序）可以进行区域特异性 DNA 甲基化分析。本章提供了亚硫酸氢盐介导的转化、BeadChip 阵列方法（Infinium）、定量 MSP 和亚硫酸氢盐测序的方案。
